scholarly journals T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Falk Lüsebrink ◽  
Alessandro Sciarra ◽  
Hendrik Mattern ◽  
Renat Yakupov ◽  
Oliver Speck
Keyword(s):  
Brain Mri ◽  
Brain Magnetic Resonance Imaging ◽  
Brain Atlas ◽  
7 Tesla ◽  
Ultrahigh Resolution ◽  
Raw Data ◽  
Whole Brain ◽  
Isotropic Resolution ◽  
High Magnetic Field Strength

Abstract We present an ultrahigh resolution in vivo human brain magnetic resonance imaging (MRI) dataset. It consists of T1-weighted whole brain anatomical data acquired at 7 Tesla with a nominal isotropic resolution of 250 μm of a single young healthy Caucasian subject and was recorded using prospective motion correction. The raw data amounts to approximately 1.2 TB and was acquired in eight hours total scan time. The resolution of this dataset is far beyond any previously published in vivo structural whole brain dataset. Its potential use is to build an in vivo MR brain atlas. Methods for image reconstruction and image restoration can be improved as the raw data is made available. Pre-processing and segmentation procedures can possibly be enhanced for high magnetic field strength and ultrahigh resolution data. Furthermore, potential resolution induced changes in quantitative data analysis can be assessed, e.g., cortical thickness or volumetric measures, as high quality images with an isotropic resolution of 1 and 0.5 mm of the same subject are included in the repository as well.

scholarly journals Erratum: T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Falk Lüsebrink ◽  
Alessandro Sciarra ◽  
Hendrik Mattern ◽  
Renat Yakupov ◽  
Oliver Speck
Keyword(s):  
Brain Mri ◽  
Whole Brain ◽  
Isotropic Resolution

scholarly journals Whole-Brain High-Resolution Metabolite Mapping with 3D Compressed-Sensing-SENSE-LowRank 1H FID-MRSI

2020 ◽  
Author(s):  
Antoine Klauser ◽  
Paul Klauser ◽  
Frédéric Grouiller ◽  
Sebastien Courvoisier ◽  
Francois Lazeyras
Keyword(s):  
High Resolution ◽  
Brain Regions ◽  
Low Rank ◽  
Acquisition Time ◽  
Resonance Spectroscopy ◽  
Brain Anatomy ◽  
Reconstruction Technique ◽  
Whole Brain ◽  
Isotropic Resolution

There is a growing interest of the neuroscience community to map the distribution of brain metabolites in vivo. Magnetic resonance spectroscopy imaging (MRSI) is often limited by either a poor spatial resolution and/or a long acquisition time which severely limits its applications for clinical or research purposes. We developed a novel acquisition-reconstruction technique combining fast 1H-FID-MRSI sequence accelerated by random k-space undersampling and a low-rank and total-generalized variation (TGV) constrained model. This framework was applied to the brain of four healthy volunteers. Following 20 min acquisition, reconstruction and quantification, the resulting metabolic maps with a 5 mm isotropic resolution reflected the detailed neurochemical composition of all brain regions and revealed part of the underlying brain anatomy. Contrasts and features from the 3D metabolite distributions were in agreement with the literature and consistent across the four subjects. The successful combination of the 3D 1H-FID-MRSI with a constrained reconstruction enables the detailed mapping of metabolite concentrations at high-resolution in the whole brain and with an acquisition time that is compatible with clinical or research settings.

scholarly journals Mapping the human subcortical auditory system using histology, post mortem MRI and in vivo MRI at 7T

2019 ◽  
Author(s):  
Kevin Richard Sitek ◽  
Omer Faruk Gulban ◽  
Evan Calabrese ◽  
G. Allan Johnson ◽  
Agustin Lage-Castellanos ◽  
...  
Keyword(s):  
Auditory System ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Auditory Pathway ◽  
7 Tesla ◽  
Post Mortem ◽  
Subcortical Structures ◽  
Isotropic Resolution ◽  
Histological Data

AbstractStudying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. We addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and post mortem MRI (50 μm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 μm isotropic resolution) and post mortem (200 μm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

scholarly journals High resolution atlas of the venous brain vasculature from 7 T quantitative susceptibility maps

2018 ◽  
Author(s):  
Julia Huck ◽  
Yvonne Wanner ◽  
Audrey P. Fan ◽  
Anna-Thekla Jäger ◽  
Sophia Grahl ◽  
...  
Keyword(s):  
Human Brain ◽  
Blood Oxygen Level Dependent ◽  
7 Tesla ◽  
Cerebral Vein ◽  
Registration Method ◽  
Isotropic Resolution ◽  
Common Location ◽  
Susceptibility Maps ◽  
Venous Vasculature

AbstractThe vascular organization of the human brain can determine neurological and neurophysiological functions, yet thus far it has not been comprehensively mapped. Aging and diseases such as dementia are known to be associated with changes to the vasculature and normative data could help detect these vascular changes in neuroimaging studies. Furthermore, given the well-known impact of venous vessels on the blood oxygen level dependent (BOLD) signal, information about the common location of veins could help detect biases in existing datasets. In this work, a quantitative atlas of the venous vasculature using quantitative susceptibility maps (QSM) acquired with a 0.6 mm isotropic resolution is presented. The Venous Neuroanatomy (VENAT) atlas was created from 5 repeated 7 Tesla MRI measurements in young and healthy volunteers (n = 20, 10 females, mean age = 25.1 ± 2.5 years) using a two-step registration method on 3D segmentations of the venous vasculature. This cerebral vein atlas includes the average vessel location, diameter (mean: 0.84 ± 0.33 mm) and curvature (0.11 ± 0.05 mm−1) from all participants and provides an in vivo measure of the angio-architectonic organization of the human brain and its variability. This atlas can be used as a basis to understand changes in the vasculature during aging and neurodegeneration, as well as vascular and physiological effects in neuroimaging.

scholarly journals Genetically defined cellular correlates of the baseline brain MRI signal

2018 ◽  
Vol 115 (41) ◽  
pp. E9727-E9736 ◽  
Author(s):  
Jie Wen ◽  
Manu S. Goyal ◽  
Serguei V. Astafiev ◽  
Marcus E. Raichle ◽  
Dmitriy A. Yablonskiy
Keyword(s):  
Functional Connectivity ◽  
Human Brain ◽  
Brain Activity ◽  
Brain Mri ◽  
Blood Oxygenation ◽  
Brain Atlas ◽  
Functional Connections ◽  
Fmri Signal ◽  
Useful Signal

fMRI revolutionized neuroscience by allowing in vivo real-time detection of human brain activity. While the nature of the fMRI signal is understood as resulting from variations in the MRI signal due to brain-activity-induced changes in the blood oxygenation level (BOLD effect), these variations constitute a very minor part of a baseline MRI signal. Hence, the fundamental (and not addressed) questions are how underlying brain cellular composition defines this baseline MRI signal and how a baseline MRI signal relates to fMRI. Herein we investigate these questions by using a multimodality approach that includes quantitative gradient recalled echo (qGRE), volumetric and functional connectivity MRI, and gene expression data from the Allen Human Brain Atlas. We demonstrate that in vivo measurement of the major baseline component of a GRE signal decay rate parameter (R2t*) provides a unique genetic perspective into the cellular constituents of the human cortex and serves as a previously unidentified link between cortical tissue composition and fMRI signal. Data show that areas of the brain cortex characterized by higher R2t* have high neuronal density and have stronger functional connections to other brain areas. Interestingly, these areas have a relatively smaller concentration of synapses and glial cells, suggesting that myelinated cortical axons are likely key cortical structures that contribute to functional connectivity. Given these associations, R2t* is expected to be a useful signal in assessing microstructural changes in the human brain during development and aging in health and disease.

scholarly journals The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
D. A. Barrière ◽  
R. Magalhães ◽  
A. Novais ◽  
P. Marques ◽  
E. Selingue ◽  
...  
Keyword(s):  
Rat Brain ◽  
Ex Vivo ◽  
Brain Mri ◽  
Brain Structures ◽  
Isotropic Resolution ◽  
Complete Set ◽  
Multimodal Mri ◽  
Preclinical Mri ◽  
Neuroimaging Software

AbstractPreclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies. Unfortunately, these techniques still suffer from a lack of dedicated and standardized neuroimaging tools, namely brain templates and descriptive atlases. Here, we present two rat brain MRI templates and their associated gray matter, white matter and cerebrospinal fluid probability maps, generated from ex vivo $${\mathrm{T}}_2^ \ast$$T2*-weighted images (90 µm isotropic resolution) and in vivo T2-weighted images (150 µm isotropic resolution). In association with these templates, we also provide both anatomical and functional 3D brain atlases, respectively derived from the merging of the Waxholm and Tohoku atlases, and analysis of resting-state functional MRI data. Finally, we propose a complete set of preclinical MRI reference resources, compatible with common neuroimaging software, for the investigation of rat brain structures and functions.

scholarly journals Comprehensive ultrahigh resolution whole brain in vivo MRI dataset as a human phantom

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Falk Lüsebrink ◽  
Hendrik Mattern ◽  
Renat Yakupov ◽  
Julio Acosta-Cabronero ◽  
Mohammad Ashtarayeh ◽  
...  
Keyword(s):  
Diffusion Tensor ◽  
Proton Density ◽  
Resonance Imaging ◽  
Quantitative Susceptibility Mapping ◽  
Ultrahigh Resolution ◽  
Isotropic Resolution ◽  
Comprehensive Collection ◽  
Weighted Magnetic Resonance Imaging ◽  
Magnetic Resonance Imaging Mri

AbstractHere, we present an extension to our previously published structural ultrahigh resolution T1-weighted magnetic resonance imaging (MRI) dataset with an isotropic resolution of 250 µm, consisting of multiple additional ultrahigh resolution contrasts. Included are up to 150 µm Time-of-Flight angiography, an updated 250 µm structural T1-weighted reconstruction, 330 µm quantitative susceptibility mapping, up to 450 µm structural T2-weighted imaging, 700 µm T1-weighted back-to-back scans, 800 µm diffusion tensor imaging, one hour continuous resting-state functional MRI with an isotropic spatial resolution of 1.8 mm as well as more than 120 other structural T1-weighted volumes together with multiple corresponding proton density weighted acquisitions collected over ten years. All data are from the same participant and were acquired on the same 7 T scanner. The repository contains the unprocessed data as well as (pre-)processing results. The data were acquired in multiple studies with individual goals. This is a unique and comprehensive collection comprising a “human phantom” dataset. Therefore, we compiled, processed, and structured the data, making them publicly available for further investigation.

In vivo demonstration of whole-brain multislice multispoke parallel transmit radiofrequency pulse design in the small and large flip angle regimes at 7 Tesla

2016 ◽  
Vol 78 (3) ◽  
pp. 1009-1019 ◽  
Author(s):  
Vincent Gras ◽  
Alexandre Vignaud ◽  
Alexis Amadon ◽  
Franck Mauconduit ◽  
Denis Le Bihan ◽  
...  
Keyword(s):  
Flip Angle ◽  
7 Tesla ◽  
Whole Brain ◽  
Pulse Design ◽  
Parallel Transmit ◽  
Radiofrequency Pulse

scholarly journals In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fuyixue Wang ◽  
Zijing Dong ◽  
Qiyuan Tian ◽  
Congyu Liao ◽  
Qiuyun Fan ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Parallel Imaging ◽  
Brain Structures ◽  
Test Bed ◽  
Whole Brain ◽  
Isotropic Resolution ◽  
Imaging Reconstruction ◽  
Further Development ◽  
Array Coil

AbstractWe present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy participant. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.

scholarly journals Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Kevin R Sitek ◽  
Omer Faruk Gulban ◽  
Evan Calabrese ◽  
G Allan Johnson ◽  
Agustin Lage-Castellanos ◽  
...  
Keyword(s):  
Auditory System ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Auditory Pathway ◽  
7 Tesla ◽  
Post Mortem ◽  
Subcortical Structures ◽  
Isotropic Resolution ◽  
Postmortem Mri

Studying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. Wfe addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and postmortem MRI (50 µm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2 mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 µm isotropic resolution) and post mortem (200 µm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

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